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Los Angeles, CA, United States

The University of Southern California is a private, not-for-profit, nonsectarian, research university founded in 1880 with its main campus in the city area of Los Angeles, California. As California's oldest private research university, USC has historically educated a large number of the region's business leaders and professionals. In recent decades, the university has also leveraged its location in Los Angeles to establish relationships with research and cultural institutions throughout Asia and the Pacific Rim. In 2011, USC was named among the Top 10 Dream Colleges in the nation. It holds a vast array of trademarks and wordmarks to the term "USC."For the 2012-2013 academic year, there were 18,316 students enrolled in four-year undergraduate programs. USC is also home to 21,642 graduate and professional students in a number of different programs, including business, law, social work, and medicine. The university has a "very high" level of research activity and received $560.9 million in sponsored research from 2009 to 2010. USC sponsors a variety of intercollegiate sports and competes in the National Collegiate Athletic Association as a member of the Pacific-12 Conference. Members of the sports teams, the Trojans, have won 100 NCAA team championships, ranking them third in the nation, and 378 NCAA individual championships, ranking them second in the nation. Trojan athletes have won 287 medals at the Olympic games , more than any other university in the world. If USC were a country, it would rank 12th in most Olympic gold medals. Wikipedia.

Lieber M.R.,University of Southern California
Annual Review of Biochemistry | Year: 2010

Double-strand DNA breaks are common events in eukaryotic cells, and there are two major pathways for repairing them: homologous recombination (HR) and nonhomologous DNA end joining (NHEJ). The various causes of double-strand breaks (DSBs) result in a diverse chemistry of DNA ends that must be repaired. Across NHEJ evolution, the enzymes of the NHEJ pathway exhibit a remarkable degree of structural tolerance in the range of DNA end substrate configurations upon which they can act. In vertebrate cells, the nuclease, DNA polymerases, and ligase of NHEJ are the most mechanistically flexible and multifunctional enzymes in each of their classes. Unlike repair pathways for more defined lesions, NHEJ repair enzymes act iteratively, act in any order, and can function independently of one another at each of the two DNA ends being joined. NHEJ is critical not only for the repair of pathologic DSBs as in chromosomal translocations, but also for the repair of physiologic DSBs created during variable (diversity) joining [V(D)J] recombination and class switch recombination (CSR). Therefore, patients lacking normal NHEJ are not only sensitive to ionizing radiation (IR), but also severely immunodeficient. © 2010 by Annual Reviews. All rights reserved. Source

Mi H.,University of Southern California
Nature protocols | Year: 2013

The PANTHER (protein annotation through evolutionary relationship) classification system (http://www.pantherdb.org/) is a comprehensive system that combines gene function, ontology, pathways and statistical analysis tools that enable biologists to analyze large-scale, genome-wide data from sequencing, proteomics or gene expression experiments. The system is built with 82 complete genomes organized into gene families and subfamilies, and their evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models or HMMs). Genes are classified according to their function in several different ways: families and subfamilies are annotated with ontology terms (Gene Ontology (GO) and PANTHER protein class), and sequences are assigned to PANTHER pathways. The PANTHER website includes a suite of tools that enable users to browse and query gene functions, and to analyze large-scale experimental data with a number of statistical tests. It is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. In the 2013 release of PANTHER (v.8.0), in addition to an update of the data content, we redesigned the website interface to improve both user experience and the system's analytical capability. This protocol provides a detailed description of how to analyze genome-wide experimental data with the PANTHER classification system. Source

Laird P.W.,University of Southern California
Nature Reviews Genetics | Year: 2010

Methylation of cytosine bases in DNA provides a layer of epigenetic control in many eukaryotes that has important implications for normal biology and disease. Therefore, profiling DNA methylation across the genome is vital to understanding the influence of epigenetics. There has been a revolution in DNA methylation analysis technology over the past decade: analyses that previously were restricted to specific loci can now be performed on a genome-scale and entire methylomes can be characterized at single-base-pair resolution. However, there is such a diversity of DNA methylation profiling techniques that it can be challenging to select one. This Review discusses the different approaches and their relative merits and introduces considerations for data analysis. © 2010 Macmillan Publishers Limited. All rights reserved. Source

Thomas D.,University of Southern California
Nature Reviews Genetics | Year: 2010

Despite the yield of recent genome-wide association (GWA) studies, the identified variants explain only a small proportion of the heritability of most complex diseases. This unexplained heritability could be partly due to geneĝ€"environment (GÃ-E) interactions or more complex pathways involving multiple genes and exposures. This Review provides a tutorial on the available epidemiological designs and statistical analysis approaches for studying specific GÃ-E interactions and choosing the most appropriate methods. I discuss the approaches that are being developed for studying entire pathways and available techniques for mining interactions in GWA data. I also explore methods for marrying hypothesis-driven pathway-based approaches with 'agnostic' GWA studies. © 2010 Macmillan Publishers Limited. All rights reserved. Source

Valente T.W.,University of Southern California
Science | Year: 2012

The term "network interventions" describes the process of using social network data to accelerate behavior change or improve organizational performance. In this Review, four strategies for network interventions are described, each of which has multiple tactical alternatives. Many of these tactics can incorporate different mathematical algorithms. Consequently, researchers have many intervention choices at their disposal. Selecting the appropriate network intervention depends on the availability and character of network data, perceived characteristics of the behavior, its existing prevalence, and the social context of the program. Source

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